LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-356-gfb9a39f1cf-modified)
  using 1 OpenMP thread(s) per MPI task
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014

# ------------------------ INITIALIZATION ----------------------------

units 		metal
dimension	3
boundary	p	p	p
atom_style	full

# ----------------------- ATOM DEFINITION ----------------------------

fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
Reading data file ...
  orthogonal box = (0 0 0) to (24.09597 24.09597 24.09597)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  432 atoms
  scanning bonds ...
  1 = max bonds/atom
  orthogonal box = (0 0 0) to (24.09597 24.09597 24.09597)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  216 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     1 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.004 seconds

group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells

neighbor 2.0 bin
comm_modify vel yes

# ------------------------ FORCE FIELDS ------------------------------

pair_style   born/coul/dsf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D
pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl

bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0

# ------------------------ Equilibration Run -------------------------------

reset_timestep 0

thermo 50
thermo_style custom step etotal pe ke temp press              epair evdwl ecoul elong ebond fnorm fmax vol

compute CSequ all temp/cs cores shells

# output via chunk method

#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector

thermo_modify temp CSequ

# velocity bias option

velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 22
  ghost atom cutoff = 22
  binsize = 11, bins = 3 3 3
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair born/coul/dsf/cs, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
velocity all scale 1427 temp CSequ

fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ

# 2 fmsec timestep

timestep 0.002
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.833 | 8.833 | 8.833 Mbytes
   Step         TotEng         PotEng         KinEng          Temp          Press          E_pair         E_vdwl         E_coul         E_long         E_bond         Fnorm           Fmax          Volume    
         0  -635.80596     -675.46362      39.657659      1427          -21302.622     -675.46362      1.6320365     -677.09565      0              0              1.3517686e-14  2.942091e-15   13990.5      
        50  -633.9898      -666.02679      32.036991      1152.7858     -4578.5691     -668.50431      37.800202     -706.30452      0              2.4775243      14.568095      4.301237       13990.5      
       100  -631.89604     -661.96149      30.065443      1081.8437     -3536.6705     -664.61797      39.185835     -703.80381      0              2.6564897      14.677938      3.9051029      13990.5      
       150  -630.08723     -662.95879      32.871559      1182.816      -109.19705     -665.76772      46.247817     -712.01554      0              2.8089272      15.270064      2.9328964      13990.5      
       200  -628.55895     -663.97376      35.414807      1274.3296     -1748.3378     -666.58436      41.73857      -708.32293      0              2.6105987      14.148339      3.104785       13990.5      
       250  -627.28761     -661.92274      34.635125      1246.2744     -1280.4784     -664.91697      43.045494     -707.96246      0              2.9942314      14.248534      2.4694691      13990.5      
       300  -626.61631     -663.65651      37.040208      1332.8164     -1887.9056     -666.35215      40.849639     -707.20179      0              2.6956393      13.142644      1.9263235      13990.5      
       350  -625.76781     -664.66441      38.896604      1399.615      -1839.4784     -667.47659      40.999217     -708.47581      0              2.812179       13.60118       1.9262783      13990.5      
       400  -625.02585     -661.46042      36.434563      1311.0235     -868.20627     -664.40232      43.213979     -707.6163       0              2.9419082      14.945422      2.7493354      13990.5      
       450  -624.32781     -660.50846      36.180654      1301.8871     -2203.3948     -663.49896      40.008667     -703.50763      0              2.9905045      14.158829      1.7299698      13990.5      
       500  -623.56254     -661.33838      37.775836      1359.2864     -810.46725     -664.11648      42.994084     -707.11056      0              2.7780988      13.686857      2.911447       13990.5      
Loop time of 4.01505 on 1 procs for 500 steps with 432 atoms

Performance: 21.519 ns/day, 1.115 hours/ns, 124.532 timesteps/s, 53.798 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.9276     | 3.9276     | 3.9276     |   0.0 | 97.82
Bond    | 0.00048873 | 0.00048873 | 0.00048873 |   0.0 |  0.01
Neigh   | 0.06123    | 0.06123    | 0.06123    |   0.0 |  1.53
Comm    | 0.019678   | 0.019678   | 0.019678   |   0.0 |  0.49
Output  | 0.00020731 | 0.00020731 | 0.00020731 |   0.0 |  0.01
Modify  | 0.004437   | 0.004437   | 0.004437   |   0.0 |  0.11
Other   |            | 0.001423   |            |       |  0.04

Nlocal:            432 ave         432 max         432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           9280 ave        9280 max        9280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         297636 ave      297636 max      297636 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 297636
Ave neighs/atom = 688.97222
Ave special neighs/atom = 1
Neighbor list builds = 20
Dangerous builds = 0

unfix thermoberendsen

# ------------------------ Dynamic Run -------------------------------

run 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.835 | 8.835 | 8.835 Mbytes
   Step         TotEng         PotEng         KinEng          Temp          Press          E_pair         E_vdwl         E_coul         E_long         E_bond         Fnorm           Fmax          Volume    
       500  -623.56254     -661.33838      37.775836      1359.2864     -810.46725     -664.11648      42.994084     -707.11056      0              2.7780988      13.686857      2.911447       13990.5      
       550  -623.5004      -660.74469      37.244293      1340.16       -1413.4021     -663.99671      41.875098     -705.87181      0              3.252018       15.098187      2.2784019      13990.5      
       600  -623.46963     -659.61733      36.147692      1300.701      -521.46881     -662.54995      43.956126     -706.50607      0              2.9326194      14.996292      2.6334285      13990.5      
       650  -623.49291     -661.50631      38.013406      1367.8349     -1230.1159     -664.21011      42.027947     -706.23805      0              2.7037929      13.982867      1.6246858      13990.5      
       700  -623.49129     -660.11541      36.624116      1317.8442     -728.01408     -663.24903      43.413147     -706.66218      0              3.1336189      15.010024      2.0564476      13990.5      
       750  -623.50292     -657.95874      34.455815      1239.8223      637.951       -661.16865      46.542898     -707.71155      0              3.2099138      15.260488      2.1844009      13990.5      
       800  -623.51763     -659.92046      36.402839      1309.882      -912.90866     -662.84996      42.668231     -705.5182       0              2.9294998      13.577878      2.0018257      13990.5      
       850  -623.44095     -660.92026      37.479312      1348.6166     -544.4885      -664.07712      43.682102     -707.75922      0              3.1568565      14.840642      2.2789179      13990.5      
       900  -623.46372     -661.22659      37.762863      1358.8196      1262.5385     -664.53188      47.660362     -712.19224      0              3.3052904      15.056924      1.8861497      13990.5      
       950  -623.50145     -660.63232      37.130868      1336.0786      1751.5973     -663.52562      48.686592     -712.21222      0              2.8933028      15.495597      2.2629636      13990.5      
      1000  -623.5019      -660.00018      36.498275      1313.316       223.45737     -663.28838      45.365214     -708.6536       0              3.2882059      14.790837      2.4233396      13990.5      
      1050  -623.45876     -660.60459      37.145824      1336.6167     -1466.8183     -663.79399      41.316211     -705.1102       0              3.1894061      14.310192      2.3144697      13990.5      
      1100  -623.51296     -661.13548      37.622524      1353.7698      1705.4105     -663.95694      48.42509      -712.38203      0              2.8214648      15.452811      3.171843       13990.5      
      1150  -623.51774     -662.76577      39.248026      1412.2602      1297.2152     -665.70043      47.251772     -712.9522       0              2.9346594      13.832045      2.1218742      13990.5      
      1200  -623.49314     -660.11411      36.62097       1317.731       448.13236     -663.14165      45.856313     -708.99797      0              3.0275422      15.255442      2.8425274      13990.5      
      1250  -623.46193     -660.3087       36.846773      1325.856      -605.86917     -663.81874      43.340631     -707.15937      0              3.5100411      15.656151      2.661373       13990.5      
      1300  -623.47385     -661.20364      37.72979       1357.6296      1676.9464     -664.54073      48.42547      -712.9662       0              3.33709        15.272139      2.1571496      13990.5      
      1350  -623.5014      -659.9413       36.439899      1311.2155      614.72133     -663.33535      46.121687     -709.45704      0              3.3940509      15.826636      3.0112309      13990.5      
      1400  -623.45215     -660.428        36.975843      1330.5003     -236.01749     -663.93341      44.162592     -708.096        0              3.505413       15.093857      2.210909       13990.5      
      1450  -623.46256     -658.54321      35.080651      1262.3057      419.39014     -661.80307      45.671786     -707.47486      0              3.2598604      14.265923      1.7983748      13990.5      
      1500  -623.46238     -659.95716      36.494777      1313.1902      1201.872      -663.60463      47.651664     -711.2563       0              3.6474778      15.489847      3.1414243      13990.5      
Loop time of 8.12325 on 1 procs for 1000 steps with 432 atoms

Performance: 21.272 ns/day, 1.128 hours/ns, 123.103 timesteps/s, 53.181 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.9441     | 7.9441     | 7.9441     |   0.0 | 97.79
Bond    | 0.0010298  | 0.0010298  | 0.0010298  |   0.0 |  0.01
Neigh   | 0.13179    | 0.13179    | 0.13179    |   0.0 |  1.62
Comm    | 0.04079    | 0.04079    | 0.04079    |   0.0 |  0.50
Output  | 0.00040781 | 0.00040781 | 0.00040781 |   0.0 |  0.01
Modify  | 0.0020719  | 0.0020719  | 0.0020719  |   0.0 |  0.03
Other   |            | 0.003095   |            |       |  0.04

Nlocal:            432 ave         432 max         432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           9245 ave        9245 max        9245 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         297140 ave      297140 max      297140 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 297140
Ave neighs/atom = 687.82407
Ave special neighs/atom = 1
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:12
